The hosts wasted the opening 45 minutes, which was void of any threat at either end of the pitch, before coming alive in the second half, as Josh Sims, Cedric Soares and Nathan Redmond were all denied chances.
Sofiane Boufal, however, missed arguably Saints best opportunity of the game for the hosts when his header drifted wide of the goal with less than a quarter hour until full-time.
A point leaves Southampton sitting precariously outside the drop zone in 17th -- a single point above Crystal Palace -- with nine games remaining in the Premier League season.
Sims, whose last two league starts have come more than 15 months apart, nearly made an impact in a dreary first half when he burst towards goal.
A slight delay allowed Bruno Martins Indi to recover enough to block an attempt cross into the box nine minutes before the break.
Badou Ndiaye tried to pull Stoke from beneath the cut line with a header only for Alex McCarthy to prevent the chance with a fine save.
Jack Butland then kept Sims and Redmond at bay, before breathing a heavy sigh of relief when he saw Boufal nod just wide nearing full-time.
Southampton: McCarthy, Bertrand, Hoedt, Stephens, Cedric, Romeu, Lemina, Redmond, Tadic (Gabbiadini 64), Sims (Boufal 76), Carrillo (Long 79).
Unused subs: Forster (GK), Bednarek, Hojbjerg, Ward-Prowse.
Stoke City: Butland, Martins Indi, Zouma, Cameron, Stafylidis (Crouch 46), Bauer, Ndiaye Allen, Choupo-Moting (Jese 64), Shaqiri, Diouf (Pieters 23).
Unused subs: Haugaard (GK), Fletcher, Johnson, Shawcross.
Bookings: Cameron (41).